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- PDB-4qqp: Crystal structure of C1QL3 mutant D207A -

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Basic information

Entry
Database: PDB / ID: 4qqp
TitleCrystal structure of C1QL3 mutant D207A
ComponentsComplement C1q-like protein 3
KeywordsPROTEIN BINDING / Jelly roll fold / C1q / Brain-specific angiogenesis inhibitor G-protein coupled receptor 3 / extracellular
Function / homology
Function and homology information


postsynaptic density assembly / collagen trimer / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of synapse organization / synaptic cleft / hippocampal mossy fiber to CA3 synapse / glutamatergic synapse / extracellular region / identical protein binding
Similarity search - Function
: / C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Jelly Rolls ...: / C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Complement C1q-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.464 Å
AuthorsRessl, S. / Brunger, A.T.
CitationJournal: Structure / Year: 2015
Title: Structures of C1q-like Proteins Reveal Unique Features among the C1q/TNF Superfamily.
Authors: Ressl, S. / Vu, B.K. / Vivona, S. / Martinelli, D.C. / Sudhof, T.C. / Brunger, A.T.
History
DepositionJun 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C1q-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8117
Polymers15,1371
Non-polymers6746
Water2,396133
1
A: Complement C1q-like protein 3
hetero molecules

A: Complement C1q-like protein 3
hetero molecules

A: Complement C1q-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,43421
Polymers45,4103
Non-polymers2,02318
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area6210 Å2
ΔGint-50 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.590, 76.590, 126.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-201-

CD

21A-202-

CD

31A-203-

CD

41A-304-

HOH

51A-316-

HOH

61A-323-

HOH

71A-375-

HOH

81A-398-

HOH

91A-404-

HOH

101A-409-

HOH

111A-423-

HOH

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Components

#1: Protein Complement C1q-like protein 3 / C1q and tumor necrosis factor-related protein 13 / C1q/TNF-related protein 13 / CTRP13 / Gliacolin


Mass: 15136.782 Da / Num. of mol.: 1 / Mutation: D207A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: C1ql3, C1ql, Ctrp13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ESN4
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG400, 0.1 Na-acetate, 0.01M CdCl2, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2013
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.46→45.72 Å / Num. obs: 22351 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.464→45.719 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 18.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 1148 5.15 %random
Rwork0.172 ---
all0.172 ---
obs0.1739 22274 89.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.464→45.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 6 133 1153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071063
X-RAY DIFFRACTIONf_angle_d1.1441444
X-RAY DIFFRACTIONf_dihedral_angle_d12.617379
X-RAY DIFFRACTIONf_chiral_restr0.054150
X-RAY DIFFRACTIONf_plane_restr0.006189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.464-1.53060.26641600.22452669X-RAY DIFFRACTION92
1.5306-1.61130.20061450.19272678X-RAY DIFFRACTION92
1.6113-1.71230.18591580.17192658X-RAY DIFFRACTION92
1.7123-1.84450.21071440.16432708X-RAY DIFFRACTION92
1.8445-2.03010.19241410.15972624X-RAY DIFFRACTION89
2.0301-2.32390.19951560.15742614X-RAY DIFFRACTION90
2.3239-2.92780.2021290.17672595X-RAY DIFFRACTION87
2.9278-45.74150.19851150.17182580X-RAY DIFFRACTION83
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.27820.12180.07361.1892-0.24983.17190.0306-0.0065-0.0247-0.0057-0.0074-0.00820.12060.06110.1180.06890.00690.01280.0475-0.01460.008345.633555.221722.5154
26.39911.60282.06573.20370.48592.55910.04830.1214-0.3595-0.01360.1138-0.06840.14670.0637-0.18970.04250.0139-0.0220.1084-0.00180.158354.783955.190139.465
31.50430.51230.61621.41110.79881.94520.01910.0837-0.276-0.0204-0.0121-0.12890.2430.1526-0.09890.08240.0287-0.00130.0555-0.00990.098249.913953.564225.0277
40.971-0.1823-0.58640.845-0.07730.8585-0.0120.0187-0.0383-0.08920.0138-0.10620.07930.14180.10950.05470.00370.00840.0791-0.0110.006451.978261.083319.0333
50.3270.1549-0.07490.9007-0.09450.97460.0349-0.1923-0.0810.19140.0144-0.06570.06380.07860.03940.06730.0088-0.00820.08820.02210.033748.027961.786640.4273
61.7072-0.3552-0.8830.75250.31540.48180.1075-0.03220.1112-0.09210.0116-0.2242-0.16380.1482-0.02350.0568-0.01920.02490.11530.01490.070156.025270.389326.9935
70.53670.1635-0.20390.96280.00721.6860.0096-0.1646-0.06720.16140.02460.02270.0235-0.05-0.02460.06890.00480.00010.08870.01180.031443.375364.517741.215
82.7584-1.8968-1.06031.32920.61150.95930.02340.22350.0577-0.1753-0.0173-0.2295-0.07760.1326-0.01260.0794-0.01510.04320.10040.0040.086554.180669.325516.2831
90.8622-0.38590.08481.1022-0.48953.5915-0.0504-0.0805-0.22020.0164-0.00770.03690.13150.0754-0.01030.04630.0142-0.00030.07570.02310.07852.235759.418134.5331
100.4934-0.0764-0.06980.3253-0.04711.0943-0.04440.034-0.0213-0.05260.00520.01570.0814-0.0541-0.09510.06910.00180.0090.05970.004-0.002943.771360.532622.7105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:16)
2X-RAY DIFFRACTION2(chain A and resid 17:22)
3X-RAY DIFFRACTION3(chain A and resid 23:36)
4X-RAY DIFFRACTION4(chain A and resid 37:56)
5X-RAY DIFFRACTION5(chain A and resid 57:73)
6X-RAY DIFFRACTION6(chain A and resid 74:82)
7X-RAY DIFFRACTION7(chain A and resid 83:99)
8X-RAY DIFFRACTION8(chain A and resid 100:107)
9X-RAY DIFFRACTION9(chain A and resid 108:122)
10X-RAY DIFFRACTION10(chain A and resid 123:137)

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